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08-09-2011, 05:54 AM
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#1 |
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Member
Location: sweden Join Date: Jun 2011
Posts: 13
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SRMA error
Hi,
First time using SRMA and right the way into error...  typical.Anyhow, here it is: Code:
java -jar -Xmx2g ../srma-0.1.15.jar I=sorted.bam O=SRMA.bam R=chr17.fasta [Tue Aug 09 14:42:24 CEST 2011] srma.SRMA INPUT=[sorted.bam] OUTPUT=[SRMA.bam] REFERENCE=chr17.fasta OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=3 MAXIMUM_TOTAL_COVERAGE=100 CORRECT_BASES=false USE_SEQUENCE_QUALITIES=true QUIET_STDERR=false MAX_HEAP_SIZE=8192 MAX_QUEUE_SIZE=65536 GRAPH_PRUNING=false NUM_THREADS=1 TMP_DIR=/tmp/ VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false Allele coverage cutoffs: coverage: 1 minimum allele coverage: 0 coverage: 2 minimum allele coverage: 0 coverage: 3 minimum allele coverage: 0 coverage: 4 minimum allele coverage: 1 coverage: 5 minimum allele coverage: 1 coverage: 6 minimum allele coverage: 1 coverage: 7 minimum allele coverage: 2 coverage: 8 minimum allele coverage: 2 coverage: 9 minimum allele coverage: 3 coverage: >9 minimum allele coverage: 3 Records processsed: 1 (last 17:3217-3266)java.lang.Exception: Error. Soft clipping with color-space data not currently supported. at srma.Align.align(Align.java:134) at srma.SRMA$AlignThread.run(SRMA.java:659) Please report bugs to srma-help@lists.sourceforge.net help would be appreciated! thanks |
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08-09-2011, 07:51 AM
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#2 |
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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The release does not support soft-clipping in color space data. There is an experimental branch in the GIT repository called "cs-soft" that you can test out. I am assuming you mapped with SHRiMP. If you cannot get soft-clipping to work, use BFAST or another mapper.
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08-09-2011, 07:58 AM
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#3 |
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Member
Location: sweden Join Date: Jun 2011
Posts: 13
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Thanks for quick answer. I'll test "cs-soft".
For mapping I used novoalign. |
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08-16-2011, 02:55 AM
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#4 |
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Member
Location: sweden Join Date: Jun 2011
Posts: 13
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Little update:
"cs-soft" worked fine on novoalign produced bam file. By the way, I was compiling it with latest samtools jar instead of recommended older version. It worked. Then I as well made alignment of same data using BFAST run it through SRMA. I got quite a few error saying: Code:
Exception in thread "main" java.lang.StackOverflowError
at java.util.ArrayList$SubList.add(ArrayList.java:928)
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08-16-2011, 07:52 AM
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#5 |
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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I am not sure how to do it (google would) but have you increased your stack size?
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08-18-2011, 05:01 AM
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#6 |
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Member
Location: sweden Join Date: Jun 2011
Posts: 13
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StackOverflow error solved. In case anybody else runs in similar problem:
-Xss[amount of mem]m flag does the job. Easy, when you know
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08-19-2011, 08:09 AM
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#7 |
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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Excellent, thank-you for posting back your solution.
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